"It was a pretty extreme beer for its day," said co-founder Rich Doyle. "Much more bitter than what people were used to, but still really balanced. It just worked."
Consumers may have been confused by the style at first, but once they tried it, they were hooked.
(Read more: First tulips, then housing...Is beer bubble next?)
"People just kept coming back to it. By the next summer, we had to keep it year 'round due to popular demand," Kenary added.
Twenty years after its debut, Harpoon IPA remains the brewery's best-selling beer, making up more than half of its sales.
"I never thought it would be popular and we didn't make it to be popular," said Doyle. "But it became the growth engine of the company."
Someone who remembers the early impact of Harpoon IPA is Mitch Steele, a brewer with Stone Brewing Co. in San Diego and the author of "IPA: Brewing Techniques, Recipes and the Evolution of the India Pale Ale." Prior to working at Stone, Steele lived in New England and was brewing at Anheuser-Busch's Merrimack, N.H., facility.
"It was a first for me, seeing a craft-brewed IPA being as popular as it was," said Steele. "Harpoon's IPA was just everywhere."
Steele now brews and formulates some of the most popular IPAs in the industry at Stone Brewing Co., the leader in West Coast-style IPAs, which are known for their extreme hop character and higher alcohol content.
(Read more: The booming beer brand trying to be the next Corona)
In comparison to many IPAs on the marketplace today, Harpoon's once "extreme" IPA now seems more approachable to the mainstream beer drinker. It's a reflection, Steele said, of the change in people's palettes and taste preferences.
"Sierra Nevada saw it with their Pale Ale. That beer was so out there when it first came out and now people look at it as just kind of a normal style of beer," he said. "It's just kind of the natural progression as people's tastes get more extreme."
While Harpoon has kept the original IPA recipe the same, it has continued to experiment with the IPA style throughout the years, releasing a Black IPA, a White IPA, Rye IPA and an Imperial IPA.
Decades later, Harpoon's Doyle said he isn't surprised that IPA has become the dominate style of beer in his industry.
"I don't know what took so long for people to catch up to us," he said. "But I'm happy it found us and we found it when we did."
—By CNBC's Tom Rotunno. Follow him on Twitter